WIG Output Functions {HMMcopy} | R Documentation

## WIG Output Functions

### Description

Fast fixedStep WIG file formatting and output

### Usage

    rangedDataToWig(correctOutput, file, column = "copy", sample = "R",
      verbose = TRUE)
    rangedDataToSeg(correctOutput, file, column = "copy", sample = "R",
      verbose = TRUE)

### Arguments

`correctOutput` | `RangedData` object for output, default options expect output from `correctReadcount`.
`file` | Filepath to write output to.
`column` | Column in input object to export. Defaults to corrected copy number.
`sample` | Sample name of the exported dataset, defaults to “R”
`verbose` | Set to FALSE to suppress messages.

### Details

Assumes that all ranges in data set are non-overlapping windows of fixed width covering the entire genome. Note that positions in WIG files are 1-based while those in SEG files are 0-based.

### Author(s)

Daniel Lai

### References

WIG

  http://genome.ucsc.edu/goldenPath/help/wiggle.html

SEG

  http://www.broadinstitute.org/igv/SEG

### See Also

`correctReadcount` output is the intended input

### Examples

      data(tumour) # Load tumour_copy
      rangedDataToWig(tumour_copy, file = "test.wig")
      rangedDataToSeg(tumour_copy, file = "test.seg")

[Package HMMcopy version 1.30.0 Index]